Mycobacterium tuberculosis (TB) is a contagious, largely pulmonary, disease that is spread through the air. Only a small number of TB bacilli are needed to cause an infection. Almost a third of the world's population is currently infected with TB. Of the people who are infected with TB but who are not infected with HIV, some 5-10% become sick or are infectious at some period during their lifetime (WHO Fact Sheet, November, 2010, WHO report 2011: Global Tuberculosis Control). People with HIV are much more likely to develop TB. An estimated 1.7 million people died from TB in 2009. Also, multidrug-resistant M. tuberculosis, MDR-TB, is spreading [Orenstein, et al., Lancet Infect. Dis. 9, 153-161 (2009); Russell, et al., Science 328, 852-856 (2010); Dye, et al., Science 328, 856-861; (2010)]. Further complicating the TB picture worldwide is the emergence of extensively drug-resistant tuberculosis, XDR-TB and extremely drug-resistant tuberculosis, XXDR-TB (WHO: Drug Resistant TB, 2012).
However, there have been relatively few new agents discovered in the last 40 years to treat TB [Aristoff, et al., Tuberculosis 90, 94-118 (2010), Koul., et al., Nature 469, 483-490 (2100)]. Among the most used TB drugs are rifampin and its analogs, isoniazid, pyrazinamide, ethambutol and fluoroquinolone. The drug pipeline today is relatively thin with only 10 new or repurposed drugs in clinical trials [Zumla, et al., Nat. Rev. Drug Discov. 11, 171-172 (2012); New TB Drugs Website, 2011, online; Sundaramurthi, et al., Tuberculosis 92, 133-138 (2012); Luetkemeyer, et al., Am. J. Respir. Crit. Care Med. 184, 1107-1113 (2011); Lienhardt, et al., Curr. Opin. Pulm. Med. 16, 186-193 (2010); Ma, et al., Lancet, 375, 2100-2109 (2010)]. One of those drugs [bedaquiline, also referred to as R207910, TMC207, Andries, et al., Science 307, 223-227 (2005), Koul, et al., CA2529265A1; Porstmann, F. R., et al., WO2006125769A1; Brickner, S. J., et al., WO2010026526A1; Devito, et al., WO2011139832A2] was approved by the FDA in December 2012 as part of a combination treatment regimen for MDR-TB (NDA 204-384). Examples of other drugs in the clinical phase of development include: gatifloxacin [Ma, et al., Lancet 375, 2100-2109 (2010), He, et al., CN102198138A, Patel, et al., WO2011101710A1, Ismail, et al., WO2012057599A1]; moxifloxacin [Ji, et al., Antimicrob. Agents Chemother. 42, 2066-2069 (1998), Miyazaki, et al., Antimicrob. Agents Chemother. 43, 85-89 (1999), Alvirez-Freites, et al., Antimicrob. Agents Chemother. 46, 1022-1025 (2002), Bosche, et al., WO2000027398A1; McCarthy, et al., WO2003099229A2; Zeldis, et al., WO2010093588A1]; sudoterb [Ginsberg, Drugs 70, 2201-2214 (2010), Arora, et al., WO2004026828A1, Arora, et al., WO2006109323A1]; PNU100480 [Williams, et al., Antimicrob. Agents Chemother. 53, 1314-1319 (2009), Barbachyn, et al., WO9507271A1, Watts, et al., WO2002002121A2; Brickner, et al., WO2010026526A1, Wallis, WO2010122456A1]; AZD5847 [Williams, et al., Antimicrob. Agents Chemother. 53, 1314-1319 (2009), Kim, et al., WO2012144790A1]; SQ109 [Protopopova, et al., J. Antimicrob. Chemother. 56, 968-974 (2005), Sutcliffe, WO2007133803A2, Meng, Q., et al., CN101468958A]; OPC67683 [Singh, et al., Science 322, 1392-1395 (2008), Singh, et al., WO2007133803A2]; PA824 [Singh, et al., Science 322, 1392-1395 (2008), Sutcliffe, WO2007133803A2, Papadopoulou, et al., US20080076797A1, Singh, et al., WO2008005651A2, Devito, et al., WO2011139832A2].
MDR-TB is resistant to isoniazid and rifampin, the two drugs that are used commonly for drug-susceptible TB and with treatment-adherent TB patients. MDR-TB that has also developed resistance to one of the injectable second line TB drugs (kanamycin, capreomycin or amikacin) and also to a fluoroquinolone drug is classed as XDR-TB. XDR-TB can be treated with other second-line TB drugs, but the treatment is more difficult, more expensive and there may be more side effects. XXDR-TB is resistant to both first line and second line TB drugs and is extremely difficult to treat. In general, treatment for all drug-resistant TB can be complicated, lengthy and may be problematic, in part because of issues of toxicity.
Our research work on retroviral integrase inhibitors has led to the discovery of highly active compounds against a diverse set of primary HIV-1 isolates [Nair, et al., US 2012 0282218 A1, Nair, et al., PCT International Patent Application No. WO 2011/071849 A2, Nair, et al., ASM ICAAC Conference H2-801 (2011)]. In investigating the molecular modeling details of the mechanism of action of our active integrase inhibitors, it was apparent that these inhibitors had one common feature, i.e., they were all interacting with the DDE catalytic triad and also with two divalent magnesium ions in the catalytic core domain of HIV integrase. The DDE motif is essential for integrase catalysis [Nair, et al., Rev. Med. Virol. 17, 277-295 (2007), Nair, et al., J. Med. Chem. 49, 445-447 (2006), Frankel, et al., Annu. Rev. Biochem. 67, 1-25 (1998)]. However, our best integrase inhibitors of this class, while exhibiting potent anti-HIV activity [Nair, et al., US 2012 0282218 A1, Nair, et al., PCT International Patent Application No. WO 2011/071849 A2, Nair, et al., ASM ICAAC Conference H2-801 (2011], did not show as compelling a level of anti-MDR TB activity as the novel compounds of the current invention.
The catalytic core domain of DNA-dependent RNA polymerase (RNAP) of bacteria is conserved among cellular organisms [Archambault, et al., Microbiol. Mol. Biol Rev. 57, 703-724 (1993)]. Examination of the crystal structure [Zhang, et al., Cell 98, 811-824 (1999)] of the RNAP of Thermus acquaticus (a model for TB RNAP), with bound rifampin, a first-line drug for TB, shows that rifampin binds to the β-site on the RNAP and inhibits RNA synthesis by blocking the path of the elongating RNA, which is believed to be its mechanism of action [Campbell, et al., Cell 104, 901-912 (2001)]. However, there are other sites existing on TB RNAP that could be targeted by inhibitors to interfere with this RNAP's functional mechanism. For example, there is a pocket on the TB RNAP catalytic core domain that contains a structural region that bears some resemblance to the catalytic triad area of the catalytic core domain of HIV-1 integrase [Frankel, et al., Annu. Rev. Biochem. 67, 1-25 (1998), Cox and Nair, Antimicrob. Agents Chemother. 17, 343-353 (2006)]. This is the β′-site of this RNAP, which is close to 18 Å away from the binding location of rifampin in the β-site. Computational chemical biology and molecular modeling experiments revealed that our novel anti-TB compounds described in this invention are capable of binding inside the catalytic channel of the RNAP β′-pocket, interacting with a Mg2+ ion and a number of other residues in the β′-pocket, as well as with a few residues that are in the structural region that forms the interface between β′- and β-pockets. Our compounds appear to bind to the TB RNAP holoenzyme either before or after binding of the promoter DNA, which produces obstruction of transcription, resulting in failure of RNAP catalysis to initiate transcription. It is relevant to state that our compounds are not alternate substrates or transition state mimics of the RNAP polymerization reaction.
The new class of compounds described in this invention are multifunctional and are designed with the following structural components: dibenzyl pyridinone scaffold, diketo-enolic functionality, and a piperazine carboxamide moiety that carries an aromatic or substituted aromatic group on the second piperazine nitrogen. The compounds have been designed as treatments for MDR-TB and have therapeutic applications in XDR-TB and XXDR-TB. An example is shown below (Figure 1). This compound is active against MDR-TB with a minimum inhibitory concentration (MIC, i.e., the lowest concentration to completely inhibit growth of MDR-TB) of <1 microgram/mL (Agar dilution susceptibility method). In addition, this compound exhibits significant in vitro anti-HIV activity in cell culture with EC90 (concentration for 90% inhibition of virus replication) in the nM range.
